From allenday at ucla.edu Mon Nov 17 12:24:33 2003 From: allenday at ucla.edu (Allen Day) Date: Mon Nov 17 12:20:51 2003 Subject: [Bioperl-microarray] Re: Bio::Microarray In-Reply-To: <000401c3ad2f$0e250080$34167680@Vivek> Message-ID: Nigam, That's excellent. I'm CCing this mail to the bioperl-microarray mailing list, as others may have comments. Can you please attach a copy of your modules in your reply so I can take a look at what you have? -Allen On Mon, 17 Nov 2003, Nigam Shah wrote: > Hi! Allen, > > I have written a module for Reading and processing GenePix GPR files. I > contacted Brian Osborn and he suggested I get in touch with you. The module > can do the following: > > 1- read a GPR file > 2- ouput user specified columns > 3- cross check the GPR file with GAL file (Gene array list file) > 4- output the GPR file header > 5- Flag data rows using six different quality filters > 6- calculate normalization factors (Spike and whole chip) > 7- Normalize the data and write user selected columns in output > 8- give a Ratio-Intensity plot (a very commonly used QC plot) for: > - all spots > - unflagged spots > - positive control spots (spikes) > > I need some help about how to write documentation, write tests and other > conventions to follow to contribute it under Bio::microarray. > > Regards, > Nigam. > > > Nigam Shah > Graduate Fellow, > Huck Institute for Life Sciences, > Penn State University. > Ph:(814)863-5720 > Web: www.personal.psu.edu/nhs109/ > > > From allenday at ucla.edu Mon Nov 17 14:34:57 2003 From: allenday at ucla.edu (Allen Day) Date: Sun Jan 18 21:45:46 2004 Subject: [Bioperl-microarray] RE: Bio::Microarray (fwd) Message-ID: ---------- Forwarded message ---------- Date: Mon, 17 Nov 2003 13:53:52 -0500 From: Nigam Shah To: 'Allen Day' Subject: RE: Bio::Microarray Hi! Allen, Here is the module, along with a test script Test_Gpr.pl and 5 files required for the test. The Test_Gpr.pl has explainations as to what each function does and what input they needs. There will be two output files written. Regards, Nigam. %-----Original Message----- %From: Allen Day [mailto:allenday@ucla.edu] %Sent: Monday, November 17, 2003 12:25 PM %To: Nigam Shah %Cc: bioperl-microarray@bioperl.org %Subject: Re: Bio::Microarray % % %Nigam, % %That's excellent. I'm CCing this mail to the %bioperl-microarray mailing %list, as others may have comments. Can you please attach a %copy of your %modules in your reply so I can take a look at what you have? % %-Allen % % %On Mon, 17 Nov 2003, Nigam Shah wrote: % %> Hi! Allen, %> %> I have written a module for Reading and processing GenePix %GPR files. %> I contacted Brian Osborn and he suggested I get in touch %with you. The %> module can do the following: %> %> 1- read a GPR file %> 2- ouput user specified columns %> 3- cross check the GPR file with GAL file (Gene array list file) %> 4- output the GPR file header %> 5- Flag data rows using six different quality filters %> 6- calculate normalization factors (Spike and whole chip) %> 7- Normalize the data and write user selected columns in output %> 8- give a Ratio-Intensity plot (a very commonly used QC plot) for: %> - all spots %> - unflagged spots %> - positive control spots (spikes) %> %> I need some help about how to write documentation, write tests and %> other conventions to follow to contribute it under Bio::microarray. %> %> Regards, %> Nigam. %> %> %> Nigam Shah %> Graduate Fellow, %> Huck Institute for Life Sciences, %> Penn State University. %> Ph:(814)863-5720 %> Web: www.personal.psu.edu/nhs109/ %> %> %> % % -------------- next part -------------- A non-text attachment was scrubbed... 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